Monday, January 25, 2016

I used to work for the New South Wales Institute of Technology, which in the late 1980s mutated into the University of Technology Sydney (UTS). During this process it acquired an organization called the College of Traditional Chinese Medicine. This group was placed in the Faculty of Science, for lack of anywhere else to put it.

The presence of Traditional Chinese Medicine (TCM) in an Australian university setting is relevant to today's blog post, because Australia seems to be one of the few places to have shown any interest in connecting TCM and Western science. Indeed, there is also a Uniclinic of Traditional Chinese Medicine within the School of Science and Health at Western Sydney University. Most of the interest in studying TCMs has otherwise been confined to Asia (see Dennis Normile. 2003. The new face of Traditional Chinese Medicine. Science 299: 188-190).

Recently, a group of Australian researchers decided to have a look at the content of some of the TCMs available in their country:

Some of these TCMs (12 out of 26) are registered for use with the Therapeutic Goods Administration, which regulates their use within Australia, while the other TCMs are not (which technically means that they should not have been commercially available). However, there is little in the way of pharmacovigilance of herbal medicines anywhere in the world.

All of the products were comprehensively audited for their biological (via next generation DNA sequencing), toxicological (LC-MS analysis) and heavy metal (arsenic, cadmium and lead, via SF-ICP-MS analysis) contents. For the latter two analyses the amount of material detected was also quantified.

As usual, we can use a phylogenetic network to visualize these data, which I have done using a neighbor-net network on the presence-absence data. The result is shown in the figure. TCMs that are closely connected in the network are similar to each other based on their detected contents, and those that are further apart are progressively more different from each other. The registered products are highlighted in red.

There is wide variation among the products. The seven most divergent TCMs in the network are all unregistered, with the remaining seven being more similar to the registered TCMs. Only two TCMs (TCM10 and TCM17) have no discrepancies between the detected contents and what was declared (either to the regulatory agency, or to the consumer in the form of an ingredients list).

The authors summarize this situation:

Genetic analysis revealed that 50% of samples contained DNA of undeclared plant or animal taxa, including an endangered species of Panthera (snow leopard). In 50% of the TCMs, an undeclared pharmaceutical agent was detected including warfarin, dexamethasone, diclofenac, cyproheptadine and paracetamol. Mass spectrometry revealed heavy metals including arsenic, lead and cadmium, one with a level of arsenic >10 times the acceptable limit.

This study presents genetic, toxicological, and heavy metal data that should be of serious concern to regulatory agencies, medical professionals and the public who choose to adopt TCM as a treatment option. Of the 26 TCMs investigated, all but two can be classified as non-compliant on the grounds of DNA, toxicology and heavy metals, or a combination thereof. In total, 92% were deemed non-compliant with some medicines posing a serious health risk.

Such findings are not only of concern to the consumer, but also flag the need for detailed auditing of herbal preparations prior to evaluation in clinical trials.

Tuesday, January 12, 2016

Given that we are still in the process of beginning the new year, it seems to be
in order to talk about directions — not in general, but rather in specific,
namely, about directions in language change. This is important in so far as
many processes in language evolution are directional. This means that they follow a
specific direction from a state X to a state Y, and this is frequently
attested across a large number of the languages of the world, while the opposite
process, that state Y changes to state X, is extremely rare or even
unattested.

In language evolution there are a lot of well-known and well-investigated
processes with a strong directional tendency. In sound change, for example, a
[p] can easily become an [f], whether it is in the Indo-European, the Austronesian, or
the Sino-Tibetan languages. Yet the opposite process, that an [f] becomes a [p]
is extremely rare. Similar tendencies hold for a [k] becoming a [ʧ], as in
Italian [ˈtʃɛnto] cento "hundred", going back to Latin [kɛntum] centum
"hundred", or a [g] becoming a [h], as in Czech [ɦora] hora "mountain", going
back to Proto-Slavic *gora "mountain" (Derksen 2008).

In semantic change, unidirectional tendencies can also be observed, although it
is often more difficult to identify them, let alone generalising
them. Nevertheless, I think it is a rather safe bet to claim that words which
originally mean "head" have a certain tendency to shift their meaning to denote
"(the) first, the boss" or "the upper part, the top", while the opposite shift
(that words which mean "boss" or "top" will be used to denote "head") is
very unlikely to happen. Finally, in grammatical change, or, to be more
precise, in grammaticalization (the process by which languages acquire new
grammatical categories) directionality is one of the most important constraints
(Haspelmath 2004).

Linguists usually know these tendencies very well, and they use them in their
daily work, be it when trying to reconstruct the original pronuncation of words
in unattested ancestral languages, when deciphering historical documents, or
when tracing the semantic development of words through history. Directional
changes are also important in evolutionary biology. Ratchet-like (that means:
unidirectional) processes serve as a major explanans for constructive neutral
evolution (Gray et al. 2010), direction is at the core of
lateral gene transfer, and — as David mentioned in an earlier
post
— the usage of directional (non-reversible) models in phylogenetic
reconstruction even provides an elegant way to root a tree (see also
Huelsenbeck et al. 2002).

Given the active transfer of ideas from the biological to the linguistic domain in the
last two decades, and the important role that directional processes play in
both domains, it is surprising to me that methodological transfer has so far
been almost exclusively limited to time-reversible models. The only approach
known to me that explicitly makes use of linguistic knowledge of directions
is that of Baxter (2006). In this paper, Baxter analysed
phonological mergers in Chinese dialects within a framework of Camin-Sokal
parsimony (Camin and Sokal 1965).

Phonological merger is a
specific systemic process in language evolution. When sounds change (and they
always change in some way), it may happen that two formerly distinct sounds are
pronounced in the same way. As a result, words that formerly sounded
different may suddenly sound alike, such as English write and right,
which remain different only in their spelling not pronunciation. Mergers are a prototypical
irreversible process. Once a merger has happened, speakers cannot go back,
unless they recorded the original distinction and artificially tuned their
language. But even this may be less easy than it seems — it is always easy to reduce distinctions. For example, most English speakers wouldn't have many difficulties in artificially pronouncing all instances of s as sh during a conversation. But being asked to pronounce a randomly chosen set of words with s as sh will turn out to be much more difficult. For this reason, mergers are an ideal data type for directional models of language change. Their drawback is, however, that they are difficult to determine, which may also be the reason why Baxter's approach has never been tested on other language families since then.

It may be justified to use time-reversible models for analyses that
use lexical data, especially cognate sets, as in the approaches following Gray
and Atkinson (2003), since it is difficult to determine the
impact of directional processes on lexical replacement. Furthermore, due to the
specific way the data is
sampled,
it is extremely difficult to determine directions. Yet in many other
approaches that use different types of data, especially in those cases that
model sound change processes (Hruschka et al. 2015,
Wheeler and Whiteley 2015) or grammatical change (Longobardi et al. 2013), it might have a substantial impact on the
results if directionality was explicitly modeled.

What does this mean for the directions for the New Year? I keep being surprised
by the similarities between evolutionary biology and historical linguistics, be
it the organization of information in genomes and languages, the processes
that drive evolution, the philosophical questions underlying our
investigations, or the quarrels among scholars in their fields. Unfortunately,
much of the transfer from the biological to the linguistic domain is still very
simplistic, often ignoring the specific differences between the two domains.
On the other hand, many fruitful analogies are still out there but have not yet
been properly investigated. So, as a direction for those who work in
interdisciplinary domains in this New Year, I think we should try to avoid
reinventing the wheel, and we should also pay attention to not putting wheels on
sledges.

Haspelmath, M. (2004): On directionality in language change with particular reference to grammaticalization. In: Fischer, O., M. Norde, and H. Perridon (eds.): Up and down the cline -- The nature of grammaticalization. John Benjamins Publishing Company: 17-44.